Friday, December 19, 2014

A take-off in tourism could open the door to new bird diseases (Image: Frans Lanting/National Geographic Creative)

For those who go, it's the trip of a lifetime – and
it wouldn't be complete without a selfie with penguins. But growing
tourism to the Antarctic, in combination with its warming climate, could
be placing penguins at a risk of infectious diseases.

Antarctic species are believed to have
weaker immune systems due to their long isolation from the world's
common pathogens. Humans only started visiting Antartica roughly 200
years ago.

Antarctica is no longer a stranger to human contact: more than 37,000 people visited the continent in the 2013-14 season
as part of a growing tourist industry, compared with an estimated 8000
just twenty years earlier. An additional 4400 researchers can be
accommodated simultaneously in Antarctica during peak months.

"The effects of both a growing tourism
industry and research presence will not be without consequences," says
Wray Grimaldi of the University of Otago in Dunedin, New Zealand.
"Penguins are highly susceptible to infectious diseases." She bases that
on a survey by her team of penguin diseases in captivity, reaching as
far back as 1947. It found reports of Salmonella, E. coli, West Nile virus and Avian pox virus infections, among others.

Widespread deaths

The team also found evidence of a number of
mass penguin mortality events across the Antarctic since 1969. A number
of infectious agents are implicated, including Avian pox, which killed
more than 400 gentoo penguins in 2006, and caused 60 per cent mortality
rates throughout another outbreak in 2008.

Grimaldi says disease agents may have
arrived in Antarctica via migrating birds like skuas or giant petrels,
although some pathogenic bacteria could have been introduced by humans.
There isn't enough evidence to test either possibility, she says.

Yet, as the climate warms, more birds are
expected to visit Antarctic regions, bringing their pathogens with them,
while diseases borne by other animals could expand their ranges
southwards.

But Norman Ratcliffe
of the British Antarctic Survey in Cambridge, UK, says there is not a
lot of evidence that wild penguin populations have been significantly
affected by disease, adding that the Antarctic's tourism industry has
been very active for 20 years and takes appropriate precautions.

"The tour companies are quite careful to
make sure everyone cleans their boots before they go ashore," he says.
"They don't allow any animal products to be taken ashore."

Warming warning

Grimaldi warns that climate change could help
drive the emergence of new penguin diseases in Antarctica. Claire
Christian of the Antarctic and Southern Ocean Coalition, a group of environmental NGOs, agrees.

"Climate change may result in a number of
stressors that make it more difficult for penguin populations to deal
with disease," she says. In addition to prompting the arrival of new
pathogens or species carrying pathogens, warming temperatures could have
a negative impact on food sources like krill, which might leave the
penguins less able to fight off illness, she adds.

"A coordinated monitoring system needs to
be in place," argues Grimaldi. "That way, responses can be directed by
science." Christian agrees, but she says research alone is not enough –
the countries that are signatories to the Antarctic Treaty also need to cooperate in implementing protective and precautionary measures.

Friday, December 12, 2014

A question that has intrigued
biologists is: Were teeth lost in the common ancestor of all living
birds or convergently in two or more independent lineages of birds? A
research team used the degraded remnants of tooth genes in birds to
determine that teeth were lost in the common ancestor of all living
birds more than 100 million years ago.

Birds are evolutionarily derived from theropod dinosaurs.

Credit: Image courtesy of University of California - Riverside

The absence of
teeth or "edentulism" has evolved on multiple occasions within
vertebrates including birds, turtles, and a few groups of mammals such
as anteaters, baleen whales and pangolins. Where early birds are
concerned, the fossil record is fragmentary. A question that has
intrigued biologists is: Based on this fossil record, were teeth lost in
the common ancestor of all living birds or convergently in two or more
independent lineages of birds?

A research team led by biologists at the University of California,
Riverside and Montclair State University, NJ, has found an answer. Using
the degraded remnants of tooth genes in birds to determine when birds
lost their teeth, the team reports in the Dec. 12 issue of Science that teeth were lost in the common ancestor of all living birds more than 100 million years ago.

"One of the larger lessons of our finding is that 'dead genes,' like
the remnants of dead organisms that are preserved in the fossil record,
have a story to tell," said Mark Springer, a professor of biology and
one of the lead authors of the study along with Robert Meredith at
Montclair State University who was previously a graduate student and
postdoctoral researcher in Springer's laboratory. "DNA from the crypt is
a powerful tool for unlocking secrets of evolutionary history."

Springer explained that edentulism and the presence of a horny beak are hallmark features of modern birds. "Ever since the discovery of the fossil bird Archaeopteryx
in 1861, it has been clear that living birds are descended from toothed
ancestors," he said. "However, the history of tooth loss in the ancestry
of modern birds has remained elusive for more than 150 years."

All toothless/enamelless vertebrates are descended from an ancestor
with enamel-capped teeth. In the case of birds, it is theropod
dinosaurs. Modern birds use a horny beak instead of teeth, and part of
their digestive tract to grind up and process food.

Tooth formation in vertebrates is a complicated process that involves
many different genes. Of these genes, six are essential for the proper
formation of dentin (DSPP) and enamel (AMTN, AMBN, ENAM, AMELX, MMP20).

The researchers examined these six genes in the genomes of 48 bird
species, which represent nearly all living bird orders, for the presence
of inactivating mutations that are shared by all 48 birds. The presence
of such shared mutations in dentin and enamel-related genes would
suggest a single loss of mineralized teeth in the common ancestor of all
living birds.

Springer, Meredith, and other members of their team found that the 48
bird species share inactivating mutations in both dentin-related (DSPP) and enamel-related genes (ENAM, AMELX,AMTN, MMP20), indicating that the genetic machinery necessary for tooth formation was lost in the common ancestor of all modern birds. "The presence of several inactivating mutations that are shared by
all 48 bird species suggests that the outer enamel covering of teeth was
lost around ~116 million years ago," Springer said.

On the basis of fossil and molecular evidence, the researchers
propose a two-step scenario whereby tooth loss and beak development
evolved together in the common ancestor of all modern birds. In the
first stage, tooth loss and partial beak development began on the
anterior portion of both the upper and lower jaws. The second stage
involved concurrent progression of tooth loss and beak development from
the anterior portion of both jaws to the back of the rostrum. "We propose that this progression ultimately resulted in a complete
horny beak that effectively replaced the teeth and may have contributed
to the diversification of living birds," Springer said.

The research team also examined the genomes of additional
toothless/enamelless vertebrates including three turtles and four
mammals (pangolin, aardvark, sloth, and armadillo) for inactivating
mutations in the dentin- and enamel-related genes. For comparison, the
researchers looked at the genomes of mammalian taxa with enamel-capped
teeth. "All edentulous vertebrate genomes that we examined are characterized by inactivating mutations in DSPP, AMBN, AMELX, AMTN, ENAM, and MMP20, rendering these genes non-functional," Springer said. "The dentin-related gene DSPP
is functional in vertebrates with enamelless teeth -- sloth, aardvark,
armadillo. All six genes are functional in the American alligator, a
representative of Crocodylia, the closest living relatives of birds, and
mammalian taxa with enamel capped teeth."

The research was supported, in part, by a grant to Springer from the National Science Foundation.Springer and Meredith were joined in the research by Guojie Zhang at
China National GeneBank, China; M. Thomas P. Gilbert at the University
of Copenhagen Oster Voldgade, Denmark; and Erich D. Jarvis at Duke
University Medical Center, NC.

All the scientists are coauthors with several others, including UC
Riverside biologist John Gatesy, on a second paper in the same issue of Science. This paper employs the same 48 bird genomes to ask the question: "What makes a bird a bird?"

"The new bird genomes represent a major advance given that only a
handful of bird genomes -- zebra finch, turkey, chicken and duck -- were
previously available," Springer said.

Crocodiles are the
closest living relatives of birds, sharing a common ancestor that lived
around 240 million years ago and also gave rise to the dinosaurs.

Credit: Stephen J. O'Brien, Avian Phylogenomics Group

Date:

December 11, 2014

Source:

Duke University

Summary:

The first findings of the
Avian Phylogenomics Consortium are being reported nearly simultaneously
in 29 papers -- eight papers in a Dec. 12 special issue of Science and
21 more in Genome Biology, GigaScience and other journals. The analyses
suggest some remarkable new ideas about bird evolution, including
insights into vocal learning and the brain, colored plumage, sex
chromosomes and the birds' relationship to dinosaurs and crocodiles.

The genomes of
modern birds tell a story of how they emerged and evolved after the mass
extinction that wiped out dinosaurs and almost everything else 66
million years ago. That story is now coming to light, thanks to an
ambitious international collaboration that has been underway for four
years.

The first findings of the Avian Phylogenomics Consortium are being
reported nearly simultaneously in 29 papers -- eight papers in a Dec. 12
special issue of Science and 21 more in Genome Biology, GigaScience and other journals.

Scientists already knew that the birds who survived the mass
extinction experienced a rapid burst of evolution. But the family tree
of modern birds has confused biologists for centuries and the molecular
details of how birds arrived at the spectacular biodiversity of more
than 10,000 species is barely known.

To resolve these fundamental questions, a consortium led by Guojie
Zhang of the National Genebank at BGI in China and the University of
Copenhagen, Erich D. Jarvis of Duke University and the Howard Hughes
Medical Institute and M. Thomas P. Gilbert of the Natural History Museum
of Denmark, has sequenced, assembled and compared full genomes of 48
bird species. The species include the crow, duck, falcon, parakeet,
crane, ibis, woodpecker, eagle and others, representing all major
branches of modern birds.

"BGI's strong support and four years of hard work by the entire
community have enabled us to answer numerous fundamental questions to an
unprecedented scale," said Guojie Zhang. "This is the largest whole
genomic study across a single vertebrate class to date. The success of
this project can only be achieved with the excellent collaboration of
all the consortium members."

"Although an increasing number of vertebrate genomes are being
released, to date no single study has deliberately targeted the full
diversity of any major vertebrate group," added Tom Gilbert. "This is
precisely what our consortium set out to do. Only with this scale of
sampling can scientists truly begin to fully explore the genomic
diversity within a full vertebrate class."

"This is an exciting moment," said neuroscientist Erich Jarvis. "Lots
of fundamental questions now can be resolved with more genomic data
from a broader sampling. I got into this project because of my interest
in birds as a model for vocal learning and speech production in humans,
and it has opened up some amazing new vistas on brain evolution."

This first round of analyses suggests some remarkable new ideas about bird evolution. The first flagship paper published in Science
presents a well-resolved new family tree for birds, based on
whole-genome data. The second flagship paper describes the big picture
of genome evolution in birds. Six other papers in the special issue of Science
describe how vocal learning may have independently evolved in a few
bird groups and in the human brain's speech regions; how the sex
chromosomes of birds came to be; how birds lost their teeth; how
crocodile genomes evolved; ways in which singing behavior regulates
genes in the brain; and a new method for phylogenic analysis with
large-scale genomic data.

The Avian Phylogenomics Consortium has so far involved more than 200
scientists hailing from 80 institutions in 20 countries, including the
BGI in China, the University of Copenhagen, Duke University, the
University of Texas at Austin, the Smithsonian Museum, the Chinese
Academy of Sciences, Louisiana State University and many others.

A Clearer Picture of the Bird Family Tree

Previous attempts to reconstruct the avian family tree using partial
DNA sequencing or anatomical and behavioral traits have met with
contradiction and confusion. Because modern birds split into species
early and in such quick succession, they did not evolve enough distinct
genetic differences at the genomic level to clearly determine their
early branching order, the researchers said. To resolve the timing and
relationships of modern birds, the consortium authors used whole-genome
DNA sequences to infer the bird species tree.

"In the past, people have been using 10 to 20 genes to try to infer
the species relationships," Jarvis said. "What we've learned from doing
this whole-genome approach is that we can infer a somewhat different
phylogeny [family tree] than what has been proposed in the past. We've
figured out that protein-coding genes tell the wrong story for inferring
the species tree. You need non-coding sequences, including the
intergenic regions. The protein coding sequences, however, tell an
interesting story of proteome-wide convergence among species with
similar life histories."

This new tree resolves the early branches of Neoaves (new birds) and
supports conclusions about some relationships that have been
long-debated. For example, the findings support three independent
origins of waterbirds. They also indicate that the common ancestor of
core landbirds, which include songbirds, parrots, woodpeckers, owls,
eagles and falcons, was an apex predator, which also gave rise to the
giant terror birds that once roamed the Americas.

The whole-genome analysis dates the evolutionary expansion of Neoaves
to the time of the mass extinction event 66 million years ago that
killed off all dinosaurs except some birds. This contradicts the idea
that Neoaves blossomed 10 to 80 million years earlier, as some recent
studies suggested.

Based on this new genomic data, only a few bird lineages survived the
mass extinction. They gave rise to the more than 10,000 Neoaves species
that comprise 95 percent of all bird species living with us today. The
freed-up ecological niches caused by the extinction event likely allowed
rapid species radiation of birds in less than 15 million years, which
explains much of modern bird biodiversity.

Increasingly sophisticated and more affordable genomic sequencing
technologies and the advent of computational tools for reconstructing
and comparing whole genomes have allowed the consortium to resolve these
controversies with better clarity than ever before, the researchers
say.

With about 14,000 genes per species, the size of the datasets and the
complexity of analyzing them required several new approaches to
computing evolutionary family trees. These were developed by computer
scientists Tandy Warnow at the University of Illinois at
Urbana-Champaign, Siavash Mirarab, a student at the University of Texas
at Austin and Alexis Stamatakis at the Heidelburg Institute for
Theoretical Studies. Their algorithms required the use of parallel
processing supercomputers at the Munich Supercomputing Center (LRZ), the
Texas Advanced Computing Center (TACC) and the San Diego Supercomputing
center (SDSC).

"The computational challenges in estimating the avian species tree
used around 300 years of CPU time, and some analyses required
supercomputers with a terabyte of memory," Warnow said.

The bird project also had support from the Genome 10K Consortium of
Scientists (G10K), an international science community working toward
rapidly assessing genome sequences for 10,000 vertebrate species.

"The Avian Genomics Consortium has accomplished the most ambitious
and successful project that the G10K Project has joined or endorsed,"
said G10K co-leader Stephen O'Brien, who co-authored a commentary on the
bird sequencing project appearing in GigaScience.

A Genomic Perspective of Avian Evolution and Biodiversity

For all their biological intricacies, birds are surprisingly light on
DNA. A study led by Zhang, Cai Li and the consortium authors found that
compared to other reptile genomes, avian genomes contain fewer of the
repeating sequences of DNA and lost hundreds of genes in their early
evolution after birds split from other reptiles.

"Many of these genes have essential functions in humans, such as in
reproduction, skeleton formation and lung systems," Zhang said. "The
loss of these key genes may have a significant effect on the evolution
of many distinct phenotypes of birds. This is an exciting finding,
because it is quite different from what people normally think, which is
that innovation is normally created by new genetic material, not the
loss of it. Sometimes, less is more."

From the whole chromosome level to the order of genes, this group
found that the genomic structure of birds has stayed remarkably the same
among species for more than 100 million years. The rate of gene
evolution across all bird species is also slower compared to mammals.

Yet some genomic regions display relatively faster evolution in
species with similar lifestyles or phenotypes, such as involving vocal
learning. This pattern of what is called convergent evolution may be the
underlying mechanism that explains how distant bird species evolved
similar phenotypes independently. Zhang said these analyses on
particular gene families begin to explain how birds evolved a lighter
skeleton, a distinct lung system, dietary specialties, color vision, as
well as colorful feathers and other sex-related traits.

Important Lessons

The new studies have shed light on several other questions about birds, including:

How did vocal learning evolve? Eight studies in the package examined
the subject of vocal learning. According to new evidence in the two
flagship papers, vocal learning evolved independently at least twice,
and was associated with convergent evolution in many proteins. A Science
study led by Andreas Pfenning, Alexander Hartemink, Jarvis and others
at Duke, in collaboration with researchers at the Allen Institute for
Brain Science in Seattle and the RIKEN Institute in Japan, found that
the specialized song-learning brain circuitry of vocal learning birds
(songbirds, parrots and hummingbirds) and human brain speech regions
have convergent changes in the activity of more than 50 genes. Most of
these genes are involved in forming neural connections.

Osceola Whitney,
Pfenning and Anne West, also of Duke, found in another Science
study that singing is associated with the activation of 10 percent of
the expressed genome, with diverse activation patterns in different
song-learning regions of the brain, controlled by epigenetic regulation
of the genome. Duke's Mukta Chakraborty and others found in a PLoS ONE
study that parrots have a song system within a song system, with the
surrounding song system unique to them. This might explain their greater
ability to imitate human speech. In a BMC Genomics study, Morgan
Wirthlin, Peter Lovell and Claudio Mello from Oregon Health &
Science University found unique genes in the song-control brain regions
of songbirds.

The XYZW of sex chromosomes. Just as the sex of humans is determined
by the X and Y chromosomes, the sex of birds is controlled by the Z and W
chromosomes. The W makes birds female, just as the Y makes humans male.
Most mammals share a similar evolutionary history of the Y chromosome,
which now contains many degenerated genes that no longer function and
only a few active genes related to "maleness." A Science study
led by Qi Zhou and Doris Bachtrog from the University of California,
Berkeley, and Zhang found that half of bird species still contain
substantial numbers of active genes in their W chromosomes. This
challenges the classic view that the W chromosome is a "graveyard of
genes" like the human Y.

This group also found that bird species are at drastically different
states of sex chromosome evolution. For example, the ostrich and emu,
which belong to one of the older branches of the bird family tree, have
sex chromosomes resembling their ancestors. Yet some modern birds such
as the chicken and zebra finch have sex chromosomes that contain few
active genes. This opens a new set of questions on how the diversity of
sex chromosomes may drive the diversity of sex differences in the
outward appearance of various bird species. Peacocks and peahens are
dramatically different; male and female crows are indistinguishable.

How did birds lose their teeth? In a Science study led by
Robert Meredith from Montclair State University and Mark Springer from
the University of California, Riverside, a comparison between the
genomes of living bird species and those of vertebrate species that have
teeth identified key mutations in the parts of the genome that code for
enamel and dentin, the building blocks of teeth. The evidence suggests
that five tooth-related genes were disabled within a short time period
in the common ancestor of modern birds more than 100 million years ago.

What's the connection between birds and dinosaurs? Unlike mammals,
birds (along with reptiles, fish and amphibians) have a large number of
tiny microchromosomes. These smaller packages of gene-rich material are
thought to have been present in their dinosaur ancestors. A study of
genome karyotype structure in BMC Genomics analyzed whole genomes of the
chicken, turkey, Peking duck, zebra finch and budgerigar. It found the
chicken has the most similar overall chromosome pattern to an avian
ancestor, which was thought to be a feathered dinosaur. This work was
led by Darren Griffin and Michael Romanov from the University of Kent,
and by Dennis Larkin and Marta Farré from the Royal Veterinary College,
University of London.

Another study in Science examined birds' closest living
relatives, the crocodiles. This team, led by Ed Green and Benedict Paton
from the University of California, Santa Cruz, David Ray from Texas
Tech University and Ed Braun from the University of Florida, found that
crocodiles have one of the slowest-evolving genomes. The researchers
were able to infer the genome sequence of the common ancestor of birds
and crocodilians (archosaurs) and therefore all dinosaurs, including
those that went extinct 66 million years ago.

Do differences in gene trees versus species trees matter? In the
phylogenomics flagship study by Jarvis and others, the consortium found
that no gene tree has a history exactly the same as the species tree,
partly due to a process called incomplete lineage sorting. Another Science
study, led by Tandy Warnow at the University of Texas and the
University of Illinois, and her student Siavash Mirarab, developed a new
computational approach called "statistical binning." They used this
approach to show it does not matter much that the gene trees differ from
the species tree because they were able to infer the first
coalescent-based, genome-scale species tree, combining gene trees with
similar histories to accurately infer a species tree.

Do bird genomes carry fewer virus sequences than other species?
Mammalian genomes harbor a diverse set of genomic "fossils" of past
viral infections called "endogenous viral elements" (EVEs). A study
published in Genome Biology led by Jie Cui of Duke-NUS Graduate
Medical School in Singapore, Edward Holmes of the University of Sydney
and Zhang, found that bird species had 6-13 times fewer EVE infections
in their past than mammals. This finding is consistent with the fact
that birds have smaller genomes than mammals. It also suggests birds may
either be less susceptible to viral invasions or better able to purge
viral genes.

When did colorful feathers evolve? Elaborate, colorful feathers are
thought to be evolutionarily advantageous, giving a male bird in a given
species an edge over his competitors when it comes to mating. Zhang's
flagship paper in Science, which is further analyzed by Matthew
Greenwold and Roger Sawyer from the University of South Carolina in a
companion study in BMC Evolutionary Biology, found that genes involved
in feather coloration evolved more quickly than other genes in eight of
46 bird lineages. Waterbirds have the lowest number of beta keratin
feather genes, landbirds have more than twice as many, and in
domesticated pet and agricultural bird species, there are eight times
more of these genes.

What happens to species facing extinction or recovering from
near-extinction? Birds are like the proverbial canaries in the coal mine
because of their sensitivity to environmental changes that cause
extinction. In a Genome Biology study led by Shengbin Li, Cheng
Cheng and Jun Yu from Xi'an Jiaotong University and Jarvis, researchers
analyzed the genomes of species that have recently gone nearly extinct,
including the crested ibis in Asia and the bald eagle in the Americas.
They found genes that break down environmental toxins have a higher rate
of mutations in these species and there is lower diversity of immune
system genes in endangered species. In a recovering crested ibis
population, genes involved in brain function and metabolism are evolving
more rapidly. The researchers found more genomic diversity in the
recovering population than was expected, giving greater hope for species
conservation.

The Start of Something Bigger

This sweeping genome-level comparison of an entire class of life is
being powered by frozen bird tissue samples collected over the past 30
years by museums and other institutions around the world. Samples are
sent as fingernail-sized chunks of frozen flesh mostly to Duke
University and University of Copenhagen for DNA separation. Most of the
genome sequencing and critical initial analyses of the genomes have then
been conducted by the BGI in China.

The avian genome consortium is now creating a database that will be
made publicly available in the future for scientists to study the
genetic basis of complex avian traits.

Setting up the pipeline for the large-scale study of whole genomes --
collecting and organizing tissue samples, extracting the DNA, analyzing
its quality, sequencing and managing torrents of new data -- has been a
massive undertaking. But the scientists say their work should help
inform other major efforts for the comprehensive sequencing of
vertebrate classes. To encourage other researchers to dig through this
'big data' and discover new patterns that were not seen in small-scale
data before, the avian genome consortium has released the full dataset
to the public in GigaScience, and in NCBI, ENSEMBL and CoGe databases.

Under the leadership of Dave Burt, the National Avian Research
Facility at the Roslin Institute and Edinburgh University, UK, has
created genome browser databases based on the ENSEMBL model for 48
species.

Two penguin genomes have been
sequenced and analyzed for the first time. The study reveals insights
into how these birds have been able to adapt to the cold and hostile
Antarctic environment.

Adélie penguins.

Credit: David Lambert

Two penguin genomes have been sequenced and analyzed for the first time in the open access, open data journal GigaScience.
Timely for the holiday season, the study reveals insights into how
these birds have been able to adapt to the cold and hostile Antarctic
environment.

Antarctic penguins are subject to extremely low temperatures, high
winds, and profound changes in daylight. They have developed complicated
biological systems to regulate temperature and store energy for
long-term fasting. Most studies have focused on the physiological and
behavioral aspects of their biology, but an international team of
researchers has now analyzed the DNA of two Antarctic penguins (Adélie
and emperor) relative to other bird species, revealing the genetic basis
of their adaptations and their evolutionary history in response to
climate change.

Using the historical genetic record within the DNA across bird
species, the researchers estimate that penguins first appeared around 60
million years ago. The study shows that the Adélie penguin population
increased rapidly about 150,000 years ago when the climate became
warmer, but later declined by 40% about 60,000 years ago during a cold
and dry glacial period. In contrast, the emperor penguin population
remained stable, suggesting that they were better adapted to glacial
conditions, for example, by being able to protect their eggs from
freezing temperatures and incubate them on their feet.

Cai Li, Team Lead at BGI-Shenzhen, China, said: "These different
patterns in historical population change also suggest that future
climate change may have impacts on the two penguin species. For example,
the fact that emperor penguins didn't experience the same population
boom as Adélie penguins in warm climates means that they could suffer
more from global warming, and this needs to be considered in
conservation efforts in Antarctica."

Both penguins were found to have expanded genes related to
beta-keratins -- the proteins which make up 90% of feathers. They also
had at least 13 genes responsible for a single type of beta-keratin,
which is the highest number compared to all other known bird genomes.
This would explain their importance in ensuring that penguin feathers
are short, stiff and densely packed to minimize heat loss, remain
waterproof and aid underwater flight. Likely to be responsible for
penguins' thick skin, the team also identified a gene called DSG1, which
is known to be involved in a human dermatological disease characterized
by thick skin on the palms and soles.

Fat storage is critical for penguins to withstand the cold and
survive long fasting periods -- up to four months in emperor penguins.
The two penguins were found to have exploited different adaptations for
lipid metabolism in the course of their evolution, which may also
provide insight into their contrasting abilities for coping with climate
change. The researchers found eight genes involved in lipid metabolism
in the Adélie penguin, and three in the emperor penguin.

During their evolutionary history, the wings (or forelimbs) of
penguins changed profoundly for wing-propelled diving in the water. The
team identified 17 forelimb-related genes in the penguin genomes that
had unique changes. One of the genes in particular, EVC2, showed a
larger number of genetic changes compared to other birds. Mutations of
EVC2 in humans cause Ellis-van Creveld syndrome, characterized by
short-limb dwarfism and short ribs.

Guojie Zhang, Assistant Professor at the University of Copenhagen and
Associate Director at China National GeneBank, BGI-Shenzhen, China,
said: "Penguins show distinct evolution relative to other bird species.
They can't fly, have specialized skin and feathers, degenerated wings,
and live in a cold environment in which most other birds could not
survive. Comparative genomics is a powerful tool for providing answers
on the molecular basis of these evolutionary changes and how organisms
deal with the conditions they are exposed to. Our study has revealed
several of these secrets for the two penguins."

David Lambert, Professor of Evolutionary Biology at Griffith
University, Australia, said: "Although Adélie and Emperor penguins both
breed on the Antarctic continent, they do so in very different ways. By
sequencing the genomes of two penguin species we have been able to
compare many of the genes that are responsible for these different
abilities to do the same thing -- namely to survive and breed in
Antarctica. This study is particularly important because it now provides
us with the opportunity to conduct large scale evolutionary studies of
both species."

These papers are part of a series of reports from the Avian
Phylogenomics Project that are being published in concert in multiple
journals. The authors of several Science papers will unveil new genomic results related to the avian tree of life, and a number of papers are also published in BMC Genomics, BMC Evolutionary Biology and Genome Biology.

New research suggests that
chickens and turkeys have experienced fewer gross genomic changes than
other birds as they evolved from their dinosaur ancestor.

New
research from the University of Kent suggests that chickens and turkeys
have experienced fewer gross genomic changes than other birds as they
evolved from their dinosaur ancestor.

Professor Darren Griffin and a team at the University's School of
Biosciences have conducted research that suggests that chromosomes of
the chicken and turkey lineage have undergone the fewest number of
changes compared to their ancient avian ancestor, thought to be a
feathered dinosaur.

The Kent research is part of a study by a consortium of leading
scientists into avian or bird genomes, which tell a story of species
evolution. The living descendants of dinosaurs were thought to have
undergone a rapid burst of evolution after most dinosaur species were
wiped out. The detailed family tree of modern birds has however confused
biologists for centuries and the molecular details of how birds arrived
at the spectacular biodiversity of more than 10,000 species is barely
known.

Professor Griffin explained: 'Bird genomes are distinctive in that
they have more tiny microchromosomes than any other vertebrate group.
These small packages of gene-rich material are thought to have been
present in their dinosaur ancestors.'We found that the chicken has the most similar overall chromosome pattern to its avian dinosaur ancestor.'The research, which formed part of a vast study carried out over the
past four years by the international Avian Phylogenomics Consortium,
involved the analysis of the whole genome structure of the chicken,
turkey, Pekin duck, zebra finch and budgerigar.

Professor Griffin and the other leaders of the research team ¬- Kent
colleague Dr Michael Romanov as well as Dr Denis Larkin and Dr Marta
Farré from the Royal Veterinary College, University of London -- studied
data from a total of 21 avian genomes and one reptile species. The team
focused on the six best-assembled genomes to put together a karyotype
-- organised profile -- of the dinosaur ancestor for each chromosome.

The researchers also found that the fastest rate of change had
occurred in the zebra finch and budgerigar, consistent with more rapid
speciation events in songbirds and their relatives.

Story Source:
The above story is based on materials provided by University of Kent. Note: Materials may be edited for content and length.

Saturday, December 6, 2014

Dr
Bernard Stonehouse, top, measuring and weighing king penguins, he said
the birds think of humans as a 'different' sorts of penguins that were
'less predictable, occasionally violent, but tolerable company when
sitting still and minding his own business'. Pictured below is a survey
hut Stonehouse built with a colleague

Polar scientist Bernard Stonehouse, who studied king penguins in Antarctica, has died at the aged of 88.

Stonehouse first went to the continent when he was 20 in
1946 and was one of a lucky few who survived three winters in the
bitterly cold conditions. He worked as naval pilot, a meteorologist, dog
sledder and, ultimately, a biologist.

The Telegraph told one amazing story of his survival on its
website: "On September 15, 1947, Stonehouse was on board as deputy
pilot when the base's Auster aircraft took off to mark out a safe
landing spot for a larger American twin-engined aircraft, which was
about to undertake an extensive aerial survey.

"On the return flight, however, bad weather forced him and
his two companions to make an emergency landing on sea ice, and the
aircraft turned on its back after one of its skis hit an ice hummock.
"The three men emerged unscathed but were forced to pitch camp on the
ice. They had only a small 'pup' (two-man) tent, one sleeping bag, one
inner bag and a tin of pemmican between the three of them. After somehow
surviving the first night and failing to attract the attention of a
rescue aircraft with a flare, they decided to attempt to cover the 70
miles to base on foot. On the first day they travelled ten miles, but
then the snow set in.

"For the next few days they averaged only three or four
miles a day, hauling their few belongings on a 'sledge' improvised from
the aircraft's fuel tank, taking it in turns to use the sleeping bag and
eking out the pemmican. Then they were hit by a ferocious gale which
saw them huddling together in the tiny tent for three more days.

"The gale was a mixed blessing, however, because when it
abated it had scoured the sea ice and they were able to set off again.
Seven days after their crash, they heard the welcome sound of an
aircraft circling some miles away and decided to use their last flare to
attract its attention. They were rescued by the American expedition's
Norseman aircraft. "They were extremely tired and hungry, but otherwise
largely unharmed."

Born in 1926, Stonehouse, was born in Hull and trained as a pilot. During his Antarctic expeditions, he was part of the group
know as the "lost 11", as they had to endure a winter at a base at
Stonington Island in 1949, after a relief ship failed to reach them
because of thick sea ice. When he came back to the UK, he studied
zoology and geology at university in London, however, he had already
made significant scientific discovery.

The Telegraph went on to explain: "The expedition to
Adelaide Island had made the exciting discovery of an emperor penguin
'rookery' on the Dion Islands, just off Adelaide's south coast. At that
time, only two other such rookeries were known.

"From early June 1949, Stonehouse, supported by two
companions, spent three months on the Dion Islands, living in tents in
temperatures as low as -40C, to study the penguins during the winter
breeding season, about which very little was known at the time. He
gained valuable data on the breeding behaviour and embryology of the
animals, observing their instinctive desire to hold an egg, or indeed
any object of similar size.

"On one occasion when a Leica camera was found to be
missing, the thief was spotted waddling away with a leather strap
trailing between its feet. A penguin, Stonehouse concluded, thinks that a
human is a penguin who is 'different, less predictable, occasionally
violent, but tolerable company when he sits still and minds his own
business'.